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What is the number at the end of UCSC transcripts ids represents for ?

Hi,

I'm trying to map around 70000 UCSC transcript IDs to Refseq IDs, but I was able just map 19000 of them.

I've looked at the UCSC transcript IDs, all of them have number at the end of the transcript name:

like :

uc010uxz.1
uc001vor.2
.
.

Does someone knows what does this numbers means? Dan I ignore them in mapping? Finally what is the best way to map UCSC IDs to Refseq IDs?

refseq transcript ucsc knowngene
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updated by Ram Ram • written by jack jack

2 answers

What the numbers mean, you can read in the documentation for the UCSC Genes track (paragraph "Methods"):

11. The transcript is assigned a permanent "uc" accession. If the transcript was not in the previous release of UCSC Genes, the accession ends with the suffix ".1" indicating that this is the first version of this transcript. If the transcript is identical to some transcript in the previous release of UCSC Genes, the accession is re-used with the same version number. If the transcript is not identical to any transcript in the previous release but it overlaps a similar transcript with a compatible structure, the previous accession is re-used with the version number incremented.

Hope this helps.

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updated by Ram Ram • written by Bert Overduin Bert Overduin

you can map the knownGenes to refseq using knownToRefSeq

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownToRefSeq.txt.gz" | gunzip -c | head
uc021vde.1    NR_034035
uc021vdf.1    NR_034035
uc021vdg.1    NR_034035
uc002qvr.2    NR_034035
uc021vdh.1    NR_034035
uc021vdj.1    NM_054016
uc021vdk.1    NM_001191005
uc031tgi.1    NM_001177376
uc031tgj.1    NM_001177376
uc031tgk.1    NM_001177376
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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

it's strange engough. I used this, but I only were albe to map around 19000 of my trasncript out of 73000.

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written by jack jack

but, when I eliminate the numbers after . in UCSC IDs, most of them are mapping. I wonder, what these numbers stands for?

For example I have uc002qvr.1 in my file but in KnownToRefSeq.tx ,there is uc002qvr.2.

so with ingoring the number after . , it's mapping. So is it correct that I ignore the numbers at the end of UCSC IDS?

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updated by Ram Ram • written by jack jack

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